Hi-I am trying to work out a work flow of integrating fsl and freesurfer. the basic goal is to do surface-based group analysis.
what I have now is the run1.feat, run2.feat and mean.gfeat for each subject done by FSL Feat and the processing anatomy using recon-all in freesurfer. so the question now is how to combine them.
It seems to me that one way is to (1) use reg-feat2anat to register the feat to freesurfer anatomy; (2) using mris_preproc to resample it into common surface space, and (3) using mri_glmfit to computer the mean for each subject; and repeat (2) and (3) for group analysis.
but if I want to use feat to do the whole statistics, I am not sure how should I proceed. I will still use (1) to do the registration, and use (4) feat2surf to resample each feat into common surface space. but then I am not sure how to do statistics using Feat (both fixed effect to combine two runs and random effect to combine across subjects).
any help will be greatly appreciated. Gui
Gui,
Have you had a look at the tutorial page that describes the FSL/Freesurfer integration?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
see slide #4, and session 2b.
I can't offer any other help than this, as I do not have experience performing this integration, but your approach is similar to the tutorial.
Nick
On Tue, 2007-12-18 at 16:26 -0800, Gui Xue wrote:
Hi-I am trying to work out a work flow of integrating fsl and freesurfer. the basic goal is to do surface-based group analysis.
what I have now is the run1.feat, run2.feat and mean.gfeat for each subject done by FSL Feat and the processing anatomy using recon-all in freesurfer. so the question now is how to combine them.
It seems to me that one way is to (1) use reg-feat2anat to register the feat to freesurfer anatomy; (2) using mris_preproc to resample it into common surface space, and (3) using mri_glmfit to computer the mean for each subject; and repeat (2) and (3) for group analysis.
but if I want to use feat to do the whole statistics, I am not sure how should I proceed. I will still use (1) to do the registration, and use (4) feat2surf to resample each feat into common surface space. but then I am not sure how to do statistics using Feat (both fixed effect to combine two runs and random effect to combine across subjects).
any help will be greatly appreciated. Gui _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I just updated this page to include instructions on how to do this
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat
Nick Schmansky wrote:
Gui,
Have you had a look at the tutorial page that describes the FSL/Freesurfer integration?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
see slide #4, and session 2b.
I can't offer any other help than this, as I do not have experience performing this integration, but your approach is similar to the tutorial.
Nick
On Tue, 2007-12-18 at 16:26 -0800, Gui Xue wrote:
Hi-I am trying to work out a work flow of integrating fsl and freesurfer. the basic goal is to do surface-based group analysis.
what I have now is the run1.feat, run2.feat and mean.gfeat for each subject done by FSL Feat and the processing anatomy using recon-all in freesurfer. so the question now is how to combine them.
It seems to me that one way is to (1) use reg-feat2anat to register the feat to freesurfer anatomy; (2) using mris_preproc to resample it into common surface space, and (3) using mri_glmfit to computer the mean for each subject; and repeat (2) and (3) for group analysis.
but if I want to use feat to do the whole statistics, I am not sure how should I proceed. I will still use (1) to do the registration, and use (4) feat2surf to resample each feat into common surface space. but then I am not sure how to do statistics using Feat (both fixed effect to combine two runs and random effect to combine across subjects).
any help will be greatly appreciated. Gui _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Doug Greve -
Gui Xue -
Nick Schmansky